Hi Stan, Robin, I'm the biomaRt developer, I've been reading through the email thread an am not sure if I understand what the problem is. The error is thrown by the biomaRt package as there is no attribute named 'referencedatabase_ncbi_gene' in the reactome pathway dataset. I see 'referencedatabase_entrez_gene' does exists, and think that is the attribute that the user is querying for, that should work.
Cheers, Steffen On Tue, Jun 26, 2012 at 9:52 AM, Stanley Ng <[email protected]>wrote: > Hi Robin and David, > > Thanks for looking into this issue for me. > Please let me know who would be the person to contact for questions about > the biomaRt module for R if this is taken care of by someone else. > > Thanks, > Stan > > ------------------------------ > *From:* Robin Haw [[email protected]] > *Sent:* June 26, 2012 12:47 PM > *To:* Stanley Ng > *Cc:* [email protected]; Francis Ouellette; [email protected]; Arek Kasprzyk > > *Subject:* Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error > > Hi Stanley, > > I might defer to my colleague David Croft for some additional input here. > > Robin > > From: Stanley Ng <[email protected]> > Date: Tuesday, 26 June, 2012 12:42 PM > To: Robin Haw <[email protected]> > Cc: "[email protected]" <[email protected]>, Francis Ouellette < > [email protected]>, David Croft <[email protected]>, Arek Kasprzyk < > [email protected]> > Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error > > Hi Robin, > > > > I am using the new email system here at UofT but thanks for forwarding the > email to me. > > > > I tried using the attribute name "referencedatabase_ncbi_gene" but it gave > me the following error message. Please let me know if I need a certain > version of biomaRt for my query to work or if there is another name for the > attribute (the output of listAttributes(mart) still lists > "referencedatabase_entrez_gene" and there is no mention of ncbi anywhere). > > > > I am currently using biomaRt_2.10.0 with R version 2.14.2 (2012-02-29). > > > > Command and Error: > > > entrezids = > > > getBM(attributes=c("referencedatabase_ncbi_gene"),filters="pathway_id_ > > > list",values=c(pathwayids[1]), mart=mart) > > Error in getBM(attributes = c("referencedatabase_ncbi_gene"), filters = > "pathway_id_list", : > > Invalid attribute(s): referencedatabase_ncbi_gene Please use the > function 'listAttributes' to get valid attribute names > > > > Thanks, > > Stan > > > ------------------------------ > *From:* Arek Kasprzyk [[email protected]] > *Sent:* June 26, 2012 4:38 AM > *To:* Robin Haw > *Cc:* Stanley Ng; [email protected]; Francis Ouellette; [email protected] > *Subject:* Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error > > Robin and David: > Thank you for clarifying this. It would be great if you could keep such > communications on the "users" mailing lists. There are other users who can > benefit from this information and if there is an action required with > regards to syncing BioPortal with Reactome I can coordinate with Francis so > that there are no service disruptions to the user community > > > thank you > > a > > On Tue, Jun 26, 2012 at 3:01 AM, Robin Haw <[email protected]> wrote: > >> Hi Stan, >> >> I'm glad I was able to forward the email to you. I think it should be >> "referencedatabase_ncbi_gene" instead "referencedatabase_entrez_gene". >> >> Are you using the new utoronto email system? There's some odd behaviour >> with the sending and receiving some emails with the utoronto mail system. >> So, this might explain why you did not receive the email earlier because it >> was definitely sent by our mail server and received at a number of >> different locations. >> >> If you have any other questions, please let me know. >> >> Robin >> >> >> ________________________________________ >> From: Stanley Ng [[email protected]] >> Sent: 25 June 2012 18:23 >> To: Robin Haw >> Cc: [email protected]; Francis Ouellette; [email protected] >> Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error >> >> Hi Robin, >> >> Thanks for your email. >> >> I didn't receive the below email from David Croft for some reason. >> (nothing in my inbox or junkmail folders) >> >> I have written some small R scripts to help me collect entrez gene IDs >> for each specified pathway. >> >> Do you know what is the new attribute name I should be using to get lists >> of NCBI gene IDs for pathways through the Biomart R module? >> i.e., right now i am querying for "referencedatabase_entrez_gene" but it >> doesn't work anymore, maybe it is called something else now? >> >> Commands: >> library("biomaRt") >> mart = useMart("REACTOME", dataset="pathway") >> pathwayids = >> getBM(attributes=c("stableidentifier_identifier"),filters="species_selection",values=c("Homo >> sapiens"), mart=mart) >> pathwayids = c(do.call("cbind",pathwayids)) >> entrezids = >> getBM(attributes=c("referencedatabase_entrez_gene"),filters="pathway_id_list",values=c(pathwayids[1]), >> mart=mart) >> >> Error: >> Query ERROR: caught BioMart::Exception::Usage: Attribute >> referencedatabase_entrez_gene NOT FOUND</pre> >> >> Thanks, >> Stan >> >> ________________________________________ >> From: Robin Haw [[email protected]] >> Sent: June 25, 2012 5:51 PM >> To: Stanley Ng >> Cc: [email protected]; Francis Ouellette; [email protected] >> Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error >> >> Dear Stanley, >> >> Is this still a problem? I thought we'd been able to address this issue, >> last week? >> >> If not, can you please let us know? >> >> Thanks, >> Robin >> >> ________________________________________ >> From: [email protected] [ >> [email protected]] on behalf of David Croft [ >> [email protected]] >> Sent: 22 June 2012 10:42 >> To: [email protected] >> Subject: Re: [Reactome-help] [Contact-us] Biomart query from R no longer >> working? >> >> Hi Stanley, >> >> Sorry about this problem, we got caught out by a database name change: >> Entrez gene is now NCBI gene. We have now updated our BioMart to >> reflect this, so if you run the query on our website, it should work. I >> do not have any experience with R-BioMart, you may need to experiment a >> little. >> >> Cheers, >> >> David Croft. >> > I am a PhD student working on leukemia at the university of toronto. >> > >> > About a month ago, I ran the following query which returned a list of >> entrez gene ids for the pathways that I was interested in. >> > >> > "library("biomaRt"); >> > >> > mart = useMart("REACTOME", dataset="pathway") >> > >> > pathwayids = >> getBM(attributes=c("stableidentifier_identifier"),filters="species_selection",values=c("Homo >> sapiens"), mart=mart) >> > >> > entrezids = >> getBM(attributes=c("referencedatabase_entrez_gene"),filters="pathway_id_list",values=c(pathwayids[i]), >> mart=mart)" >> > >> > However I tried to run that same query today through R biomart and it >> no longer works. I see the following error and was wondering if the query >> requirements have changed for what I am seeking? >> > >> > " >> > Error in getBM(attributes = c("referencedatabase_entrez_gene"), filters >> = "pathway_id_list", : >> > Query ERROR: caught BioMart::Exception::Query: Query error occurred >> at web service based data source! >> > >> > Remote data source: http://www.reactome.org:5555/biomart/martservice? >> > >> > Query XML: >> > <?xml version="1.0" encoding="UTF-8"?> >> > <!DOCTYPE Query> >> > <Query virtualSchemaName = "default" limitStart = "" limitSize = >> "200" count = "" softwareVersion = "0.6" requestId= "biomart-client"> >> > <Dataset name = "pathway" interface = "default" > >> > <Attribute name = >> "referencedatabase_entrez_gene" /> >> > <ValueFilter name = "pathway_id_list" value = >> "REACT_1698"/> >> > </Dataset> >> > </Query> >> > >> > Please ensure the above query XML is well-formed and does not contain >> illegal characters. >> > >> > Error message from remote server as below: >> > Query ERROR: caught BioMart::Exception::Database: Error during query >> execution: Unknown column >> 'test_reactome_mart.pathway__referencednasequence__dm.referencedatabase_entrez_gene' >> in 'field list' >> > >> > " >> > _______________________________________________ >> > Reactome-help mailing list >> > [email protected] >> > https://lists.reactome.org/mailman/listinfo/reactome-help >> >> _______________________________________________ >> Reactome-help mailing list >> [email protected] >> https://lists.reactome.org/mailman/listinfo/reactome-help >> >> ________________________________________ >> From: Stanley Ng [[email protected]] >> Sent: 25 June 2012 16:50 >> To: Robin Haw >> Cc: [email protected]; Francis Ouellette; [email protected] >> Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error >> >> Hi Robin, >> >> When do you think this can be fixed? >> >> Thanks, >> Stan >> >> ________________________________________ >> From: Stanley Ng >> Sent: June 25, 2012 3:41 PM >> To: [email protected] >> Cc: [email protected]; Robin Haw; Francis Ouellette ([email protected]) >> Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error >> >> Hi Arek, >> >> Thanks for clarifying. I had thought it may have been a new issue. >> >> Stan >> ________________________________________ >> From: arek kasprzyk [[email protected]] >> Sent: June 25, 2012 2:01 PM >> To: Stanley Ng >> Cc: [email protected]; Robin Haw; Francis Ouellette ([email protected]) >> Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error >> >> Hi Stan >> >> This is still the same problem. Hopefully Robin Haw (cc'ed on this emai)l >> will be able to help you >> >> >> Sent from my BlackBerry® smartphone on O2 >> >> -----Original Message----- >> From: Stanley Wai-Kwong Ng <[email protected]> >> Sender: [email protected] >> Date: Mon, 25 Jun 2012 13:35:19 >> To: 'Arek Kasprzyk'<[email protected]> >> Cc: <[email protected]> >> Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error >> >> _______________________________________________ >> Users mailing list >> [email protected] >> https://lists.biomart.org/mailman/listinfo/users >> >> >> >> >> > > > -- > Arek Kasprzyk, MD, MSc, PhD > BioMart Project Lead > www.biomart.org > > _______________________________________________ > Users mailing list > [email protected] > https://lists.biomart.org/mailman/listinfo/users > >
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